A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/metatdenovo analysis pipeline. For information about how to interpret these results, please see the documentation.
/cfs/klemming/projects/supr/snic2020-16-76/ddl/dev/metatdenovo/.nf-test/tests/f1cb7d92dfb67a6837ee0588018cb491/work/ca/a216a59ed29488519cd3ab34528a81
General Statistics
| Sample Name | Bases Removed (%) | Bases Removed (Mb) | Reads Removed (%) | Reads Removed (M) | Total Input Reads (M) |
|---|---|---|---|---|---|
| SAMPLE1_PE_1_val_1 | 0.1 | 0.0Mb | 0.1 | 0.0M | 0.1M |
| SAMPLE2_PE_1_val_1 | 0.3 | 0.0Mb | 0.3 | 0.0M | 0.0M |
BBDuk
Common data-quality-related trimming, filtering, and masking operations with a kmer based approach.URL: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide
BBDuk: Filtered Reads
The number of reads removed by various BBDuk filters
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| BBMAP_ALIGN | bbmap | 39.01 |
| pigz | 2.6 | |
| samtools | 1.16.1 | |
| BBMAP_BBDUK | bbmap | 39.1 |
| BBMAP_INDEX | bbmap | 39.1 |
| CAT_FASTQ | cat | 9.5 |
| COLLECT_FEATURECOUNTS | R | 4.2.3 |
| data.table | 1.14.8 | |
| dplyr | 1.1.2 | |
| dtplyr | 1.3.1 | |
| COLLECT_STATS | R | 4.2.3 |
| dplyr | 1.1.2 | |
| purrr | 1.0.1 | |
| readr | 2.1.4 | |
| stringr | 1.5.0 | |
| tidyr | 1.3.0 | |
| FASTQC | fastqc | 0.12.1 |
| FEATURECOUNTS_CDS | subread | 2.0.6 |
| FORMAT_PRODIGAL_GFF | gzip | 1.11 |
| MEGAHIT_INTERLEAVED | megahit_interleaved | 1.2.9 |
| PRODIGAL_MODULE | pigz | 2.6 |
| prodigal | 2.6.3 | |
| SAMTOOLS_FLAGSTAT | samtools | 1.21 |
| SAMTOOLS_IDXSTATS | samtools | 1.21 |
| SAMTOOLS_INDEX | samtools | 1.21 |
| SAMTOOLS_SORT | samtools | 1.21 |
| SAMTOOLS_STATS | samtools | 1.21 |
| SEQTK_MERGEPE | seqtk | 1.4-r122 |
| TRANSRATE | transrate | 1.0.3 |
| TRIMGALORE | cutadapt | 4.9 |
| pigz | 2.8 | |
| trimgalore | 0.6.10 | |
| UNPIGZ_CONTIGS | pigz | 2.3.4 |
| UNPIGZ_GFF | pigz | 2.3.4 |
| Workflow | Nextflow | 24.10.4 |
| nf-core/metatdenovo | v1.1dev |
nf-core/metatdenovo Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/metatdenovo
nf-core/metatdenovo Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/metatdenovo